Waikato industry could face "horrendous costs" trying to get approval for increasingly difficult water consents if Auckland Council's application for more water from the Waikato River is successful.

That it is the warning from Waikato Federated Farmers president, James Houghton, who has voiced concern at Auckland Council's application, through Watercare, to take 200,000 cubic metres of water a day from the river to meet the region's public demand over the next three decades.

The council organisation already siphons 150,000 cubic metres of water a day from the river but Auckland's population is expected to grow by at least 800,000 people by 2049 - exceeding the city's current supply capabilities.

If given the go ahead, authorities at Waikato Regional Council have said that Waikato applicants would face a "higher burden" to get a consent in the future and, in times of low river flow, some users might find it more difficult to get additional water.

Mr Houghton said he was worried not just for the agricultural sector, but for all businesses in the region.

Watercare's proposed take would mean the "allocable flow" of the lower river catchment would be exceeded.

But under the variation 6 of the regional plan, supply to Auckland would be prioritised during periods of low summer flow and, as a public supplier, when applications are made.

No timeframe has been provided for when the application would be processed, as consents were dealt with on a first in first served basis.

Council consented sites division manager Brent Sinclair said that the application was not a question of being granted or declined.

"The outcome is not either zero or 200,000 [cubic metres], it could be somewhere in between.

"Whilst in theory the answer could be no. Logic tells me that within the policy framework that gives importance to people, just because it's in Auckland doesn't change things."

In 2012, allocation limits were set for all rivers and streams in Waikato to manage competing demands and ensure that the environment is not degraded.

At low flow times users get asked to draw back on water to ensure the minimum flow is maintained.

Different users are asked to cut back their water use by varying degrees depending on priority.

Water take for municipal and domestic water supplies was a top priority and irrigation was at the bottom.

Similar priority was also given to different groups when they applied for consent, although where someone lived was not a factor.

Mr Sinclair said municipal and domestic supply is treated as a "discretionary activity" in a fully allocated catchment as long as it has a demand management plan.